Next-generation proteomics: towards an integrative view of proteome dynamics

Mass Spectrometry–Based Proteomics and Network Biology

(2012) Ariel Bensimon et al.   Annual Review of Biochemistry

Wnt Signaling through Inhibition of β-Catenin Degradation in an Intact Axin1 Complex

(2012) Vivian S.W. Li et al.   CELL

A Census of Human Soluble Protein Complexes

(2012) Pierre C. Havugimana et al.   CELL

Personal Omics Profiling Reveals Dynamic Molecular and Medical Phenotypes

(2012) Rui Chen et al.   CELL

Insights into RNA Biology from an Atlas of Mammalian mRNA-Binding Proteins

(2012) Alfredo Castello et al.   CELL

Sequential Application of Anticancer Drugs Enhances Cell Death by Rewiring Apoptotic Signaling Networks

(2012) Michael J. Lee et al.   CELL

Trends in ultrasensitive proteomics

(2012) AF Maarten Altelaar et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

The Lgr5 intestinal stem cell signature: robust expression of proposed quiescent ‘+4’ cell markers

(2012) Javier Muñoz et al.   EMBO JOURNAL

Role of mass spectrometry-based proteomics in the study of cellular reprogramming and induced pluripotent stem cells

(2012) Marco Benevento et al.   Expert Review of Proteomics

Chimeras taking shape: Potential functions of proteins encoded by chimeric RNA transcripts

(2012) M. Frenkel-Morgenstern et al.   GENOME RESEARCH

Proteomic Cornerstones of Hematopoietic Stem Cell Differentiation: Distinct Signatures of Multipotent Progenitors and Myeloid Committed Cells

(2012) Daniel Klimmeck et al.   MOLECULAR & CELLULAR PROTEOMICS

Proteomic Investigations Reveal a Role for RNA Processing Factor THRAP3 in the DNA Damage Response

(2012) Petra Beli et al.   MOLECULAR CELL

Interaction landscape of membrane-protein complexes in Saccharomyces cerevisiae

(2012) Mohan Babu et al.   NATURE

Proteomics: The interaction map

(2012) Monya Baker   NATURE

A high-throughput approach for measuring temporal changes in the interactome

(2012) Anders R Kristensen et al.   NATURE METHODS

Phosphorylation sites of higher stoichiometry are more conserved

(2012) Chris Soon Heng Tan et al.   NATURE METHODS

Selected reaction monitoring–based proteomics: workflows, potential, pitfalls and future directions

(2012) Paola Picotti et al.   NATURE METHODS

Protease bias in absolute protein quantitation

(2012) Mao Peng et al.   NATURE METHODS

Determination of site-specific glycan heterogeneity on glycoproteins

(2012) Daniel Kolarich et al.   Nature Protocols

Instant spectral assignment for advanced decision tree-driven mass spectrometry

(2012) D. J. Bailey et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Sensitive kinase assay linked with phosphoproteomics for identifying direct kinase substrates

(2012) L. Xue et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Computational and informatics strategies for identification of specific protein interaction partners in affinity purification mass spectrometry experiments

(2012) Alexey I. Nesvizhskii   PROTEOMICS

Structural Probing of a Protein Phosphatase 2A Network by Chemical Cross-Linking and Mass Spectrometry

(2012) F. Herzog et al.   SCIENCE

Comment on "Widespread RNA and DNA Sequence Differences in the Human Transcriptome"

(2012) C. L. Kleinman et al.   SCIENCE

Hyperplexing: A Method for Higher-Order Multiplexed Quantitative Proteomics Provides a Map of the Dynamic Response to Rapamycin in Yeast

(2012) N. Dephoure et al.   Science Signaling

Quantitative maps of protein phosphorylation sites across 14 different rat organs and tissues

(2012) Alicia Lundby et al.   Nature Communications

Performance Characteristics of a New Hybrid Quadrupole Time-of-Flight Tandem Mass Spectrometer (TripleTOF 5600)

(2011) Genna L. Andrews et al.   ANALYTICAL CHEMISTRY

Quantitative, High-Resolution Proteomics for Data-Driven Systems Biology

(2011) Jürgen Cox et al.   Annual Review of Biochemistry

Lung Cancer Signatures in Plasma Based on Proteome Profiling of Mouse Tumor Models

(2011) Ayumu Taguchi et al.   CANCER CELL

Cancer Biomarkers: Closer to Delivering on their Promise

(2011) Lance A. Liotta et al.   CANCER CELL

The Cell in an Era of Systems Biology

(2011) Paul Nurse et al.   CELL

Analysis of the Human Endogenous Coregulator Complexome

(2011) Anna Malovannaya et al.   CELL

A Protein Complex Network of Drosophila melanogaster

(2011) K.G. Guruharsha et al.   CELL

Systematic Discovery of TLR Signaling Components Delineates Viral-Sensing Circuits

(2011) Nicolas Chevrier et al.   CELL

Interactome Networks and Human Disease

(2011) Marc Vidal et al.   CELL

A ceRNA Hypothesis: The Rosetta Stone of a Hidden RNA Language?

(2011) Leonardo Salmena et al.   CELL

Shotgun proteomics aids discovery of novel protein-coding genes, alternative splicing, and "resurrected" pseudogenes in the mouse genome

(2011) M. Brosch et al.   GENOME RESEARCH

Highly Sensitive Proteome Analysis of FACS-Sorted Adult Colon Stem Cells

(2011) Serena Di Palma et al.   JOURNAL OF PROTEOME RESEARCH

High Recovery FASP Applied to the Proteomic Analysis of Microdissected Formalin Fixed Paraffin Embedded Cancer Tissues Retrieves Known Colon Cancer Markers

(2011) Jacek R. Wiśniewski et al.   JOURNAL OF PROTEOME RESEARCH

Improved Peptide Identification by Targeted Fragmentation Using CID, HCD and ETD on an LTQ-Orbitrap Velos

(2011) Christian K. Frese et al.   JOURNAL OF PROTEOME RESEARCH

Deep proteome and transcriptome mapping of a human cancer cell line

(2011) N. Nagaraj et al.   Molecular Systems Biology

The quantitative proteome of a human cell line

(2011) M. Beck et al.   Molecular Systems Biology

Bring on the biomarkers

(2011) George Poste   NATURE

Global quantification of mammalian gene expression control

(2011) Björn Schwanhäusser et al.   NATURE

A pipeline that integrates the discovery and verification of plasma protein biomarkers reveals candidate markers for cardiovascular disease

(2011) Terri A Addona et al.   NATURE BIOTECHNOLOGY

Selected reaction monitoring mass spectrometry reveals the dynamics of signaling through the GRB2 adaptor

(2011) Nicolas Bisson et al.   NATURE BIOTECHNOLOGY

A targeted proteomics–based pipeline for verification of biomarkers in plasma

(2011) Jeffrey R Whiteaker et al.   NATURE BIOTECHNOLOGY

aPKC phosphorylates NuMA-related LIN-5 to position the mitotic spindle during asymmetric division

(2011) Matilde Galli et al.   NATURE CELL BIOLOGY

Harnessing the potential of induced pluripotent stem cells for regenerative medicine

(2011) Sean M. Wu et al.   NATURE CELL BIOLOGY

Proteomic and phosphoproteomic comparison of human ES and iPS cells

(2011) Douglas H Phanstiel et al.   NATURE METHODS

Gas-phase purification enables accurate, multiplexed proteome quantification with isobaric tagging

(2011) Craig D Wenger et al.   NATURE METHODS

A large-scale method to measure absolute protein phosphorylation stoichiometries

(2011) Ronghu Wu et al.   NATURE METHODS

MS3 eliminates ratio distortion in isobaric multiplexed quantitative proteomics

(2011) Lily Ting et al.   NATURE METHODS

Database independent proteomics analysis of the ostrich and human proteome

(2011) A. F. M. Altelaar et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Exploring the Genomes of Cancer Cells: Progress and Promise

(2011) M. R. Stratton   SCIENCE

Phosphoproteomic Analysis Identifies Grb10 as an mTORC1 Substrate That Negatively Regulates Insulin Signaling

(2011) Y. Yu et al.   SCIENCE

A Cell Cycle Phosphoproteome of the Yeast Centrosome

(2011) J. M. Keck et al.   SCIENCE

Widespread RNA and DNA Sequence Differences in the Human Transcriptome

(2011) M. Li et al.   SCIENCE

Single-Cell Mass Cytometry of Differential Immune and Drug Responses Across a Human Hematopoietic Continuum

(2011) S. C. Bendall et al.   SCIENCE

Quantitative Phosphoproteomics Identifies Substrates and Functional Modules of Aurora and Polo-Like Kinase Activities in Mitotic Cells

(2011) A. N. Kettenbach et al.   Science Signaling

System-Wide Temporal Characterization of the Proteome and Phosphoproteome of Human Embryonic Stem Cell Differentiation

(2011) K. T. G. Rigbolt et al.   Science Signaling

The Reality of Pervasive Transcription

(2011) Michael B. Clark et al.   PLOS BIOLOGY

Mass Spectrometry–Based Biomarker Discovery: Toward a Global Proteome Index of Individuality

(2010) Adam M. Hawkridge et al.   Annual Review of Analytical Chemistry

Sororin Mediates Sister Chromatid Cohesion by Antagonizing Wapl

(2010) Tomoko Nishiyama et al.   CELL

Dynamics of Cullin-RING Ubiquitin Ligase Network Revealed by Systematic Quantitative Proteomics

(2010) Eric J. Bennett et al.   CELL

The Protein Composition of Mitotic Chromosomes Determined Using Multiclassifier Combinatorial Proteomics

(2010) Shinya Ohta et al.   CELL

Quantitative Interaction Proteomics and Genome-wide Profiling of Epigenetic Histone Marks and Their Readers

(2010) Michiel Vermeulen et al.   CELL

A Tissue-Specific Atlas of Mouse Protein Phosphorylation and Expression

(2010) Edward L. Huttlin et al.   CELL

Extensive In Vivo Metabolite-Protein Interactions Revealed by Large-Scale Systematic Analyses

(2010) Xiyan Li et al.   CELL

Precision Mapping of an In Vivo N-Glycoproteome Reveals Rigid Topological and Sequence Constraints

(2010) Dorota F. Zielinska et al.   CELL

Lab-Specific Gene Expression Signatures in Pluripotent Stem Cells

(2010) Aaron M. Newman et al.   Cell Stem Cell

Chromatin Structure and Gene Expression Programs of Human Embryonic and Induced Pluripotent Stem Cells

(2010) Matthew G. Guenther et al.   Cell Stem Cell

Probing Native Protein Structures by Chemical Cross-linking, Mass Spectrometry, and Bioinformatics

(2010) Alexander Leitner et al.   MOLECULAR & CELLULAR PROTEOMICS

Network organization of the human autophagy system

(2010) Christian Behrends et al.   NATURE

Global analysis of lysine ubiquitination by ubiquitin remnant immunoaffinity profiling

(2010) Guoqiang Xu et al.   NATURE BIOTECHNOLOGY

Super-SILAC mix for quantitative proteomics of human tumor tissue

(2010) Tamar Geiger et al.   NATURE METHODS

A Global Protein Kinase and Phosphatase Interaction Network in Yeast

(2010) A. Breitkreutz et al.   SCIENCE

Systematic Analysis of Human Protein Complexes Identifies Chromosome Segregation Proteins

(2010) J. R. A. Hutchins et al.   SCIENCE

Extensive Crosstalk Between O-GlcNAcylation and Phosphorylation Regulates Cytokinesis

(2010) Z. Wang et al.   Science Signaling

Akt-RSK-S6 Kinase Signaling Networks Activated by Oncogenic Receptor Tyrosine Kinases

(2010) A. Moritz et al.   Science Signaling

Elafin Is a Biomarker of Graft-Versus-Host Disease of the Skin

(2010) S. Paczesny et al.   Science Translational Medicine

Recommendations for Biomarker Identification and Qualification in Clinical Proteomics

(2010) H. Mischak et al.   Science Translational Medicine

Pathway-Based Identification of Biomarkers for Targeted Therapeutics: Personalized Oncology with PI3K Pathway Inhibitors

(2010) J. N. Andersen et al.   Science Translational Medicine

Defining the Human Deubiquitinating Enzyme Interaction Landscape

(2009) Mathew E. Sowa et al.   CELL

Full Dynamic Range Proteome Analysis of S. cerevisiae by Targeted Proteomics

(2009) Paola Picotti et al.   CELL

Phosphorylation Dynamics during Early Differentiation of Human Embryonic Stem Cells

(2009) Dennis Van Hoof et al.   Cell Stem Cell

Induced Pluripotent Stem Cells and Embryonic Stem Cells Are Distinguished by Gene Expression Signatures

(2009) Mark H. Chin et al.   Cell Stem Cell

The phosphoproteomics data explosion

(2009) Simone Lemeer et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Systems-level dynamic analyses of fate change in murine embryonic stem cells

(2009) Rong Lu et al.   NATURE

Single Lgr5 stem cells build crypt-villus structures in vitro without a mesenchymal niche

(2009) Toshiro Sato et al.   NATURE

Multi-site assessment of the precision and reproducibility of multiple reaction monitoring–based measurements of proteins in plasma

(2009) Terri A Addona et al.   NATURE BIOTECHNOLOGY

Quantitative interaction proteomics using mass spectrometry

(2009) Alexander Wepf et al.   NATURE METHODS

Multiplex peptide stable isotope dimethyl labeling for quantitative proteomics

(2009) Paul J Boersema et al.   Nature Protocols

Lysine Acetylation Targets Protein Complexes and Co-Regulates Major Cellular Functions

(2009) C. Choudhary et al.   SCIENCE

Genome-Wide Analysis in Vivo of Translation with Nucleotide Resolution Using Ribosome Profiling

(2009) N. T. Ingolia et al.   SCIENCE

SILAC Mouse for Quantitative Proteomics Uncovers Kindlin-3 as an Essential Factor for Red Blood Cell Function

(2008) Marcus Krüger et al.   CELL

Global Transcription in Pluripotent Embryonic Stem Cells

(2008) Sol Efroni et al.   Cell Stem Cell

Targeted proteomic strategy for clinical biomarker discovery

(2008) Ralph Schiess et al.   Molecular Oncology

Comprehensive mass-spectrometry-based proteome quantification of haploid versus diploid yeast

(2008) Lyris M. F. de Godoy et al.   NATURE

BAC TransgeneOmics: a high-throughput method for exploration of protein function in mammals

(2008) Ina Poser et al.   NATURE METHODS

Native mass spectrometry: a bridge between interactomics and structural biology

(2008) Albert J R Heck   NATURE METHODS

An empirical framework for binary interactome mapping

(2008) Kavitha Venkatesan et al.   NATURE METHODS

An experimentally derived confidence score for binary protein-protein interactions

(2008) Pascal Braun et al.   NATURE METHODS

The SCX/IMAC enrichment approach for global phosphorylation analysis by mass spectrometry

(2008) Judit Villén et al.   Nature Protocols

High-Quality Binary Protein Interaction Map of the Yeast Interactome Network

(2008) H. Yu et al.   SCIENCE

Non-functional phosphorylations?

(2008) Gustav E. Lienhard   TRENDS IN BIOCHEMICAL SCIENCES